scholarly journals Performance Evaluation of Manual and Automated (MagNA Pure) Nucleic Acid Isolation in HPV Detection and Genotyping Using Roche Linear Array HPV Test

2011 ◽  
Vol 2011 ◽  
pp. 1-11 ◽  
Author(s):  
Aikaterini Chranioti ◽  
Evangelia Aga ◽  
Niki Margari ◽  
Christine Kottaridi ◽  
Asimakis Pappas ◽  
...  
Keyword(s):  
Extraction Method ◽  
Area Under Curve ◽  
Linear Array ◽  
Multiple Infections ◽  
Predictive Values ◽  
Pure System ◽  
Nucleic Acid Isolation ◽  
Hpv Test ◽  
Roche Linear Array ◽  
Manual Extraction

Nucleic acids of human papillomavirus (HPV) isolated by manual extraction method (AmpliLute) and automated MagNA pure system were compared and evaluated with cytohistological findings in 253 women. The concordance level between AmpliLute and MagNA was very good 93.3% (κ=0.864,P<.0001). Overall HPVpositivity detected by AmpliLute was 57.3% (30.4% as single and 27% as multiple infections) in contrast to MagNA 54.5% (32% and 23%, resp.). Discrepant results observed in 25 cases: 11 MagNA(−)/AmpliLute(+), 10 of which had positive histology; 5 MagNA(+)/AmpliLute(−) with negative histology; 8 MagNA(+)/AmpliLute(+): in 7 of which AmpliLute detected extra HPV genotypes and 1 MagNA(invalid)/AmpliLute(+) with positive histology. Both methods performed well when compared against cytological (area under curve (AUC) of AmpliLute 0.712 versus 0.672 of MagNA) and histological diagnoses (AUC of AmpliLute 0.935 versus 0.877 of MagNA), with AmpliLute showing a slightly predominance over MagNA. However, higher sensitivities, specificities, and positive/negative predictive values were obtained by AmpliLute.

scholarly journals Evaluation of Extraction Methods for Clinical Metagenomic Assay

2020 ◽  
Vol 8 (8) ◽  
pp. 1128
Author(s):  
Suha A. Farraj ◽  
Shreif A. El-Kafrawy ◽  
Taha A. Kumosani ◽  
Jehad M. Yousef ◽  
Esam I. Azhar
Keyword(s):  
Nucleic Acid ◽  
Comparative Evaluation ◽  
Extraction Method ◽  
Extraction Methods ◽  
Multiple Infections ◽  
Infectious Agents ◽  
Nucleic Acid Isolation ◽  
Efficient Detection ◽  
Different Types ◽  
Etiological Agents

(1) Background: Clinical metagenomics is a promising approach that helps to identify etiological agents in cases of unknown infections. For the efficient detection of an unknown pathogen, the extraction method must be carefully selected for the maximum recovery of nucleic acid from different microorganisms. The aim of this study was to evaluate different extraction methods that have the ability to isolate nucleic acids from different types of pathogens with good quality and quantity for efficient use in clinical metagenomic identification. (2) Methods: A mock sample spiked with five different pathogens was used for the comparative evaluation of different commercial extraction kits. Extracted samples were subjected to library preparation and run on MiSeq. The selected extraction method based on the outcome of the comparative evaluation was used subsequently for the nucleic acid isolation of all infectious agents in clinical respiratory samples with multiple infections. (3) Results: The protocol using the PowerViral® Environmental RNA-DNA Isolation Kit with a 5-min bead beating step achieved the best results with a low starting volume. The analysis of the tested clinical specimens showed the ability to successfully identify different types of pathogens. (4) Conclusions: The optimized extraction protocol in this study is recommended for clinical metagenomics application in specimens with multiple infections from different taxa.

scholarly journals Performance of HPV16/18 in Triage of Cytological Atypical Squamous Cells of Undetermined Significance

2019 ◽  
Vol 2019 ◽  
pp. 1-6
Author(s):  
Xiaoqin Cao ◽  
Shuzheng Liu ◽  
Manman Jia ◽  
Hongmin Chen ◽  
Dongmei Zhao ◽  
...  
Keyword(s):  
Cervical Cancer ◽  
Cancer Screening ◽  
Cervical Cancer Screening ◽  
Predictive Value ◽  
Statistical Tests ◽  
Predictive Values ◽  
Squamous Cells ◽  
Link Type ◽  
Hpv Test ◽  
Undetermined Significance

Context. Human papillomavirus (HPV) testing is widely used in cervical cancer screening in women; however, its efficiency in triaging women with atypical squamous cells of undetermined significance (ASC-US) needs to be validated. Objective. To evaluate the performance of HPV16/18 in the triage of women with ASC-US. Methods. Women presenting for routine cervical cancer screening had cervical specimens collected, with which both liquid-based cytology (LBC) and hrHPVs were examined; those with ASC-US cytology underwent colposcopy. HPV16/18 and 12 other types were tested with domestic hybridization capture and chemiluminescence signal amplification (DH3). Performance characteristics of HPV test (sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV) for identification of cervical intraepithelium neoplasma (CIN) grade 2 or worse (CIN2+), and CIN grade 3 or worse (CIN3+)) were determined using standard statistical tests. Results. 317 women with ASC-US were eligible for the study. HrHPV prevalence was 15.77% (50/317); HPV16/18 prevalence was 3.61% (20/317). Sensitivity and specificity of HPV16/18 for detection of CIN 2+ were 64.71% and 97% and 64.29% and 96.37% for detection of CIN 3+, respectively. The positive predictive values (PPVs) and negative predictive values (NPVs) of HPV16/18 were 55.00% and 97.98% for CIN2+ and 45.00% and 98.32% for CIN3+, respectively. Conclusion. HPV16/18 can be considered as an effective method to triage women with ASC-US as its good clinical performance. Trial Registration. This trial is registered with Henan Cancer Hospital Medical Ethics Committee on July 5, 2016 (http://www.anti-cancer.com.cn), with registry no.: 2016037.

Use of a Linear Array for the Detection of Human Papillomavirus Genotypes in Head and Neck Cancer

2010 ◽  
Vol 134 (12) ◽  
pp. 1813-1817
Author(s):  
Candice C. Black ◽  
Heather A. Bentley ◽  
Thomas H. Davis ◽  
Gregory J. Tsongalis
Keyword(s):  
Human Papillomavirus ◽  
Head And Neck ◽  
Linear Array ◽  
Hpv Genotyping ◽  
Formalin Fixed Paraffin ◽  
Hpv Status ◽  
Test Kit ◽  
Formalin Fixed Paraffin Embedded ◽  
Roche Linear Array ◽  
Formalin Fixed

Abstract Context—Tumors of the head and neck commonly arise from the squamous and respiratory mucosa that lines the nasal and oral cavity, sinuses, pharynx, and larynx. The rate of oropharyngeal cancers diagnosed among Americans younger than 50 years is increasing. Infection of the oropharynx and tonsils by the human papillomavirus (HPV) has been linked to preneoplasia and cancer. Objectives—To evaluate the Roche Linear Array HPV Genotyping test kit to identify, and then specifically genotype, HPV in formalin-fixed, paraffin-embedded tissues. Design—We evaluated the performance of this assay for accuracy, for intra-assay and interassay precision, and for its limit of detection, using materials with known HPV status. Sixteen tumor tissues with the following origins were evaluated: 1 ocular, 1 hypopharynx, 8 tonsil, 1 retromolar trigone, 3 tongue, 1 anal, and 1 lymph node. DNA from formalin-fixed, paraffin-embedded tumor sections was isolated and amplified in duplicate, with positive and negative controls, using primers specific to the polymorphic L1 region of the HPV genome. Thirty-seven genotypes were tested using the linear array. The amplified product (450 base pairs) was visualized by gel electrophoresis and, if positive, reflexed to HPV genotyping. Results—Nine of the 16 tumors analyzed were HPV positive. The detected genotypes included HPV 6, 16, and 69. Conclusions—The Roche Linear Array HPV Genotyping test is an easy-to-use method for determining HPV genotype in the routine analysis of formalin-fixed, paraffin-embedded tumors. This assay is robust and can be performed routinely in a clinical laboratory setting.

Classification Accuracy of Curriculum-Based Measures for Beginning Writers in First Grade

2017 ◽  
Vol 43 (3) ◽  
pp. 131-143 ◽  
Author(s):  
Pyung-Gang Jung ◽  
Kristen L. McMaster
Keyword(s):  
Classification Accuracy ◽  
Area Under Curve ◽  
First Graders ◽  
First Grade ◽  
Written Language ◽  
Curriculum Based Measurement ◽  
Correct Word ◽  
Predictive Values ◽  
Curriculum Based Measures ◽  
Beginning Writers

We examined the classification accuracy of Curriculum-Based Measurement in writing (CBM-W) Picture Word prompts scored for words written (WW), words spelled correctly (WSC), and correct word sequences (CWS). First graders ( n = 133) were administered CBM-W prompts and the Test of Written Language–Third Edition (TOWL-3; Hammill & Larsen, 1996). Prompts scored for WSC showed acceptable levels of sensitivity (.947) and specificity (.587) with the TOWL-3 Contextual Language. Positive predictive values were low (approximately .20 to .30), and negative predictive values were high (mostly above .95). Overall classification accuracy, represented by the area under curve (AUC), ranged from .727 to .831. Further research regarding ways to improve classification accuracy of CBM-W and preliminary implications for practice are discussed.

scholarly journals Conservative management of CIN2p16 positive lesions in women with multiple HPV infection

2020 ◽  
Author(s):  
Maria Teresa Bruno ◽  
Guido Scalia ◽  
Nazario Cassaro ◽  
Maria Costanzo ◽  
Sara Boemi
Keyword(s):  
Laser Therapy ◽  
Conservative Management ◽  
Negative Impact ◽  
Hpv Infection ◽  
Multiple Infection ◽  
Multiple Infections ◽  
Hpv Test ◽  
American Society ◽  
The Impact

Abstract BackgroundAccording to the 2006 American Society for Colposcopy and Cervical Pathology guidelines, positive CIN2 p16 in women over the age of 25 should be managed with excisional treatment. However, excisional treatment is associated with physical, psychological and obstetric morbidity and can have a negative impact on sexual function. In our study we sought to identify a clear management strategy, addressing the impact of routine use of p16 immunohistochemistry in this population and identify appropriate criteria for patient selection with the aim of reducing over-treatment.MethodWe studied the medical records of 130 patients who had undergone laser therapy for CIN2. Each patient underwent colposcopy, biopsy and HPV test and were tested for p16 protein,. Patients were divided based on HPV infection into: single infections, multiple infections. All patients underwent ZTA laser therapy with follow-up (2-year follow-up ). Statistical analysis Contingency tables were created to evaluate the correlation between single, multiple and CIN2+ infections. Values with p <0.05 were considered statistically significant.ResultsSingle infections had a histological regression of 61.8% (21/34) and a histological persistence rate of 35.3% (12/34), which was greater than the multiple infection rate. The common characteristic that the women with persistence and progression had was the dimension of the lesion and the genotype 16. Ten cases of histological persistence and the only case of progression had one lesion greater than three quarters of the cervix.ConclusionsWith the progress of our understanding of the natural history of infection from human papillomavirus and the increasing use of colposcopy, thanks to the addition of HPV genotyping and the technique of immunohistochemistry, conservative management of these lesions is now possible

scholarly journals Multicentric study of cervical cancer screening with human papillomavirus testing and assessment of triage methods in Latin America: the ESTAMPA screening study protocol

BMJ Open ◽  
2020 ◽  
Vol 10 (5) ◽  
pp. e035796
Author(s):  
Maribel Almonte ◽  
Raúl Murillo ◽  
Gloria Inés Sánchez ◽  
Paula González ◽  
Annabelle Ferrera ◽  
...  
Keyword(s):  
Latin America ◽  
Human Papillomavirus ◽  
Study Protocol ◽  
Low Income ◽  
International Agency ◽  
Hpv Testing ◽  
Middle Income ◽  
Multicentric Study ◽  
Predictive Values ◽  
Hpv Test

IntroductionHuman papillomavirus (HPV) testing is replacing cytology in primary screening. Its limited specificity demands using a second (triage) test to better identify women at high-risk of cervical disease. Cytology represents the immediate triage but its low sensitivity might hamper HPV testing sensitivity, particularly in low-income and middle-income countries (LMICs), where cytology performance has been suboptimal. The ESTAMPA (EStudio multicéntrico de TAMizaje y triaje de cáncer de cuello uterino con pruebas del virus del PApiloma humano; Spanish acronym) study will: (1) evaluate the performance of different triage techniques to detect cervical precancer and (2) inform on how to implement HPV-based screening programmes in LMIC.Methods and analysisWomen aged 30–64 years are screened with HPV testing and Pap across 12 study centres in Latin America. Screened positives have colposcopy with biopsy and treatment of lesions. Women with no evident disease are recalled 18 months later for another HPV test; those HPV-positive undergo colposcopy with biopsy and treatment as needed. Biological specimens are collected in different visits for triage testing, which is not used for clinical management. The study outcome is histological high-grade squamous intraepithelial or worse lesions (HSIL+) under the lower anogenital squamous terminology. About 50 000 women will be screened and 500 HSIL+ cases detected (at initial and 18 months screening). Performance measures (sensitivity, specificity and predictive values) of triage techniques to detect HSIL+ will be estimated and compared with adjustment by age and study centre.Ethics and disseminationThe study protocol has been approved by the Ethics Committee of the International Agency for Research on Cancer (IARC), of the Pan American Health Organisation (PAHO) and by those in each participating centre. A Data and Safety Monitoring Board (DSMB) has been established to monitor progress of the study, assure participant safety, advice on scientific conduct and analysis and suggest protocol improvements. Study findings will be published in peer-reviewed journals and presented at scientific meetings.Trial registration numberNCT01881659

Armored target extraction method based on linear array LiDAR of terminal sensitive sub-ammunition

2019 ◽  
Vol 48 (3) ◽  
pp. 330002 ◽  
Author(s):  
武军安 Wu Jun′an ◽  
郭 锐 Guo Rui ◽  
刘荣忠 Liu Rongzhong ◽  
刘 磊 Liu Lei ◽  
柯尊贵 Ke Zungui
Keyword(s):  
Extraction Method ◽  
Linear Array ◽  
Target Extraction
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